Re: [galaxy-dev] Galaxy: Dependency error htseq_count

2013-03-22 Thread Lance Parsons
Glad that everything works now for you.  The Get Updates functionality 
won't work since this is a new version of the tool (updated version of 
HTSeq package).  Since the updated version could generate different 
results with the same input, Galaxy keeps the old version around for 
reproducibility reasons.


I don't know why you have to restart Galaxy for the tool to show up.  As 
far as I know, that should not be necessary, and also shouldn't be 
dependent on anything in the tool wrapper configuration.


I'm aware of the issue with the screenshot missing.  I'm not sure how to 
get the tool wrapper to point to the static images installed from the 
toolshed (or if that's even possible).  In the meantime, a workaround 
would be to copy the count_modes.png file from the repository to the 
[GALAXY_HOME]/static/images directory.


Lance

Joachim Jacob | VIB | wrote:

*sorry for my late reply - we have experienced some email issues lately *

Thanks, a clean install from the new versions works!

Unfortunately, the 'get updates' from the admin interface of Galaxy 
does not find any updates with the old version.


So, I searched the main toolshed, and I was able to install the new 
version next to the old (instead of updating). The install succeeded, 
but I always have to restart Galaxy to get the tool available in the 
toolbox.



One small remark: the screenshot in the tool's interface below the 
parameters is not shown.



Cheers
Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 03/11/2013 06:34 PM, Lance Parsons wrote:
I have posted an updated version of the htseq-count tool in the 
toolshed that uses and updated version of the HTSEQ count package 
(0.5.4p1) and hopefully addresses the installation issue you have 
experienced.  Please try it out and let me know if you still have 
problems.


Lance

Joachim Jacob | VIB | wrote:

Hi Lance,

[apologies for directly emailing to you and not through the 
galaxy-dev list. I will post it on the dev list later on]


I am trying to install htseq-count, but it fails during the 
dependency installation of htseq.


The error I get is:

error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in the
installation directory:

[Errno 2] No such file or directory: 
'/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' 



The installation directory you specified (via --install-dir, 
--prefix, or

the distutils default setting) was:

/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/

This directory does not currently exist. Please create it and try 
again, or
choose a different installation directory (using the -d or 
--install-dir

option).

Any idea whether it is related to my setup (and what I can do about 
it)? Note: only the htseq_count dependency is not being installed.
Thanks for providing the htseq_count wrapper! Now getting it through 
the toolshed will make it again a little closer to a perfect world :-)



Cheers,
Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 12/17/2012 05:28 PM, Lance Parsons wrote:
Thanks for looking into this Greg.  The environment where I'm 
having this problem is our testing and production systems.


Both environments are CentOS release 5.8 (Final) with Mercurial 
version 2.4.1.


Interestingly, when I tried the same thing with a development setup 
on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same 
issue. One difference is that on my testing/production boxes I do 
have an older version of the tool installed, so perhaps that is the 
issue.


I also tried uninstalling, but that led to the (expected) error 
that that a previous changeset is installed:
The tool shed repository htseq_count with owner lparsons and 
changeset revision f320093f1e8e was previously installed using 
changeset revision 5d969cb56112. The repository has been 
uninstalled, however, so reinstall the original repository instead 
of installing it again. You can get the latest updates for the 
repository using the Get updates option from the repository's 
Repository Actions pop-up menu. Click here to manage the repository.


I then attempted to reinstall and I got a javascript message the 
cloning failed, and the repo is now stuck in the cloning state.  
I did not see anything in the paster logs regarding this at all.



Here are the steps I took on my local system:

  1. Upload htseq-count v0.3 to local toolshed

  2. Install on local galaxy

  3. Upload htseq-count v0.3-release2 to toolshed

[Errno 2] No such file or directory: 
'/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' 



STDOUT from paster
 

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

2013-03-11 Thread Lance Parsons
I have posted an updated version of the htseq-count tool in the toolshed 
that uses and updated version of the HTSEQ count package (0.5.4p1) and 
hopefully addresses the installation issue you have experienced.  Please 
try it out and let me know if you still have problems.


Lance

Joachim Jacob | VIB | wrote:

Hi Lance,

[apologies for directly emailing to you and not through the galaxy-dev 
list. I will post it on the dev list later on]


I am trying to install htseq-count, but it fails during the dependency 
installation of htseq.


The error I get is:

error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in the
installation directory:

[Errno 2] No such file or directory: 
'/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' 



The installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/

This directory does not currently exist. Please create it and try 
again, or

choose a different installation directory (using the -d or --install-dir
option).

Any idea whether it is related to my setup (and what I can do about 
it)? Note: only the htseq_count dependency is not being installed.
Thanks for providing the htseq_count wrapper! Now getting it through 
the toolshed will make it again a little closer to a perfect world :-)



Cheers,
Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 12/17/2012 05:28 PM, Lance Parsons wrote:
Thanks for looking into this Greg.  The environment where I'm having 
this problem is our testing and production systems.


Both environments are CentOS release 5.8 (Final) with Mercurial 
version 2.4.1.


Interestingly, when I tried the same thing with a development setup 
on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same 
issue. One difference is that on my testing/production boxes I do 
have an older version of the tool installed, so perhaps that is the 
issue.


I also tried uninstalling, but that led to the (expected) error that 
that a previous changeset is installed:
The tool shed repository htseq_count with owner lparsons and 
changeset revision f320093f1e8e was previously installed using 
changeset revision 5d969cb56112. The repository has been uninstalled, 
however, so reinstall the original repository instead of installing 
it again. You can get the latest updates for the repository using the 
Get updates option from the repository's Repository Actions pop-up 
menu. Click here to manage the repository.


I then attempted to reinstall and I got a javascript message the 
cloning failed, and the repo is now stuck in the cloning state.  I 
did not see anything in the paster logs regarding this at all.



Here are the steps I took on my local system:

  1. Upload htseq-count v0.3 to local toolshed

  2. Install on local galaxy

  3. Upload htseq-count v0.3-release2 to toolshed

[Errno 2] No such file or directory: 
'/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' 



STDOUT from paster
 htseq-count.xml does not exist!
sam_fa_indices.loc.sample does not exist!
static/images/count_modes.png does not exist!
test-data/htseq-test-paired.bam does not exist!
test-data/htseq-test-paired_counts.tsv does not exist!
test-data/htseq-test-paired_othercounts.tsv does not exist!
test-data/htseq-test.bam does not exist!
test-data/htseq-test.gff does not exist!
test-data/htseq-test.sam does not exist!
test-data/htseq-test_counts.tsv does not exist!
test-data/htseq-test_othercounts.tsv does not exist!
tool_data_table_conf.xml.sample does not exist!
  4. Second attempt to upload
The file 'htseq-count_0.3.release2.tar.gz' has been successfully 
uncompressed and uploaded to the repository. 1 undesirable items (.hg 
.svn .git directories, .DS_Store, hgrc files, etc) were removed from 
the archive. 13 files were removed from the repository root.


  5. Get repository updates
The installed repository named 'htseq_count' has been updated to 
change set revision '74a6a8221337'.




Greg Von Kuster wrote:

Hi Lance,

I tried several scenarios today in an attempt to reproduce this but 
I was not able to.  Have you tried uninstalling the repository 
(check the checkbox to completely uninstall it) and then reinstall 
it?  I'm trying to reproduce this on a mac running mercurial version 
2.2.3 and Python 2.5.  What's your environment?


Greg Von Kuster


On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote:

Since I've had issues with workflow and the toolshed in the past, I 
have changed my workflow so that my only interaction with the 
toolshed is either via uploading a tarball via the web interface or 
installing a tool into my local Galaxy via the web 

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

2013-03-05 Thread Lance Parsons

Hi Joachim,

It seems that the error is because your system is trying to install the 
library files to lib64/python instead of just lib/python.  For reasons I 
don't quite understand, the setup.py installation fails when that 
directory doesn't exist (I would think it would just create it, but that 
doesn't appear to be the case).  As a quick fix, you might try creating 
the directory 
/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/.  
Create it as the user that galaxy runs under so make sure galaxy has 
permissions later.  Then try reinstalling the dependency.  I'm not sure 
that will work, but that is the gist of the problem.


I noticed there is an update to the htseq-count package, so I'll try to 
put out a new version of the wrapper with a fix for that as well as the 
new version.  Let me know if you still have trouble or if you find some 
sort of workaround or fix.  I'd like to make the installation more robust.


Lance

Joachim Jacob | VIB | wrote:

Hi Lance,

[apologies for directly emailing to you and not through the galaxy-dev 
list. I will post it on the dev list later on]


I am trying to install htseq-count, but it fails during the dependency 
installation of htseq.


The error I get is:

error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in the
installation directory:

[Errno 2] No such file or directory: 
'/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' 



The installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/

This directory does not currently exist. Please create it and try 
again, or

choose a different installation directory (using the -d or --install-dir
option).

Any idea whether it is related to my setup (and what I can do about 
it)? Note: only the htseq_count dependency is not being installed.
Thanks for providing the htseq_count wrapper! Now getting it through 
the toolshed will make it again a little closer to a perfect world :-)



Cheers,
Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 12/17/2012 05:28 PM, Lance Parsons wrote:
Thanks for looking into this Greg.  The environment where I'm having 
this problem is our testing and production systems.


Both environments are CentOS release 5.8 (Final) with Mercurial 
version 2.4.1.


Interestingly, when I tried the same thing with a development setup 
on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same 
issue. One difference is that on my testing/production boxes I do 
have an older version of the tool installed, so perhaps that is the 
issue.


I also tried uninstalling, but that led to the (expected) error that 
that a previous changeset is installed:
The tool shed repository htseq_count with owner lparsons and 
changeset revision f320093f1e8e was previously installed using 
changeset revision 5d969cb56112. The repository has been uninstalled, 
however, so reinstall the original repository instead of installing 
it again. You can get the latest updates for the repository using the 
Get updates option from the repository's Repository Actions pop-up 
menu. Click here to manage the repository.


I then attempted to reinstall and I got a javascript message the 
cloning failed, and the repo is now stuck in the cloning state.  I 
did not see anything in the paster logs regarding this at all.



Here are the steps I took on my local system:

  1. Upload htseq-count v0.3 to local toolshed

  2. Install on local galaxy

  3. Upload htseq-count v0.3-release2 to toolshed

[Errno 2] No such file or directory: 
'/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' 



STDOUT from paster
 htseq-count.xml does not exist!
sam_fa_indices.loc.sample does not exist!
static/images/count_modes.png does not exist!
test-data/htseq-test-paired.bam does not exist!
test-data/htseq-test-paired_counts.tsv does not exist!
test-data/htseq-test-paired_othercounts.tsv does not exist!
test-data/htseq-test.bam does not exist!
test-data/htseq-test.gff does not exist!
test-data/htseq-test.sam does not exist!
test-data/htseq-test_counts.tsv does not exist!
test-data/htseq-test_othercounts.tsv does not exist!
tool_data_table_conf.xml.sample does not exist!
  4. Second attempt to upload
The file 'htseq-count_0.3.release2.tar.gz' has been successfully 
uncompressed and uploaded to the repository. 1 undesirable items (.hg 
.svn .git directories, .DS_Store, hgrc files, etc) were removed from 
the archive. 13 files were removed from the repository root.


  5. Get repository updates
The installed repository named 'htseq_count' has been updated to 
change set revision '74a6a8221337'.